This is an interesting debate and relates to interesting jurisprudential questions about the nature of laws and the role and obligations of law enforcers.
I've read the whole thread and it seems like there are the following viewpoints:
(1) The rule is a good one and the offical was correct to enforce it. Anyone who alerted the official to the rule has no blame. The coach is to blame for not ensuring compliance.
(2) The rule is not a good one (because petty, doesn't aid fair competition or safety) but because it is on the rulebook the official, once aware of the breach had no alternative but to enforce the rule. Officials should not exercise discretion because that could lead to subjectivity and arbitrariness.. Parents who may have alerted the official to the rule have some blame, as does coach.
(3) The rule is not a good one (above reasons) and the official should have recognised its not a good rule and despite being aware of the breach used a discretion not to enforce it, in the wider interests of fairplay and the essence of the sport.
I run competitively and am a lawyer with an interest in philosophy of law. I have to admit I agree with (3). Essentially I credit humans and officials with enough wit and common sense to apply (or disapply) rules with common sense.
I have a certain limited sympathy with (2). Ideally the people who enforce rules should be different from those who make them. Ideally rules should be followed or revoked. Ideally the application of rules should not be an arbitrary choice of an official.
However, here common sense and fairness should trump (2) and prevail.
I have very little sympathy with (1). (I guess this is because I am a libertarian and generally wish for a society with fewer rules). The person who argued that the sport would be better offand taken more seriously with rules like big successful sports made an ingenious argument however.
The jews / gold star analogy and the crushed Japanese student argument are both relevant and interesting. (When did people become so scared of analogies?!) The star or david is an example of a bad rule that shouldn't be enforced because it is bad. The schoolgate example is an example of a non-bad rule that should be applied with discretion. Don't close huge metal gates when a child is running at them. It's sort of obvious.
I've lived in Japan and seen those gates.
In Britain the rules in XC is that singlets have to match. Doesn't matter if shorts/socks are different.